Add missing quotes in decoupler bseudobulk tools (#336)

Co-authored-by: Pablo Moreno <[email protected]>

tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

@@ -1,4 +1,4 @@
-<tool id="decoupler_pathway_inference" name="Decoupler Pathway Inference" version="1.4.0+galaxy1" profile="20.05" license="MIT">
+<tool id="decoupler_pathway_inference" name="Decoupler Pathway Inference" version="1.4.0+galaxy2" profile="20.05" license="MIT">
     <description>
         of functional genesets/pathways for scRNA-seq data.
     </description>
@@ -12,9 +12,9 @@
             --min_n "$min_n"
             --method '$method'
             $use_raw
-            --source $source
-            --target $target
-            --weight $weight
+            --source '$source'
+            --target '$target'
+            --weight '$weight'
             #if $gene_symbols_field:
                 --var_gene_symbols_field '$gene_symbols_field'
             #end if

tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml

@@ -1,12 +1,12 @@
-<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy7" profile="20.05">
+<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy8" profile="20.05">
     <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 mkdir deseq_output_dir &&
 mkdir plots_output_dir &&
-python '$__tool_directory__/decoupler_pseudobulk.py' $input_file
+python '$__tool_directory__/decoupler_pseudobulk.py' '$input_file'
     #if $adata_obs_fields_to_merge:
     --adata_obs_fields_to_merge '$adata_obs_fields_to_merge'
     #end if